Card Range To Study

59 Cards in this Set

In the cloverleaf structure of tRNA, the inverted sequences form _____ double-helical segments.

Four

On the tRNA, where does the amino acid bind during amino acid activation?

At the 3' end, where there is a single strand sequence -CCA- The terminal A is coupled to the amino acid during activation.

During amino acid activation, the amino acid couples with the terminal ___ base on the 3' end of the tRNA.

A; this is invariant - the CCA is almost a consensus sequence

What are the four 'arms' on tRNA molecule (3' to 5')?

1. T(psi)C arm - named for sequence T(psi)C that occurs on this arm in almost all tRNAs (psi is a modified U)
2. The variable arm; may contain between 4 and 21 nucleotides
3. Anticodon arm; contains 3 nucleotide anticodon that pairs with the codon during translation.
4. DHU arm; named for the occurence of dihydrouridine in all tRNAs

How is a charged tRNA attached to the amino acid?

It is covalently bonded.

What type of RNA can have modified bases after post-transcription modifications?

Mature tRNAs can contain modified bases other than normal A,U,G, and C.

Where is the wobble position on a tRNA molecule?

On the anticodon arm at the 5' end.

What is the significance of the wobble position?

It allows one tRNA to bond to multiple different codons.

True or False: All tRNA go through translation sites in the order of A-P-E.

False; the initial tRNA carrying methionine binds to the P site, then the E site. This is the only tRNA to do so.

The ribosome and tRNAs move in relation to the ______.

mRNA; the ribosome moves along the mRNA for the space of a single codon - the A site become the P site and the new tRNA enters and bonds to the new A site.

What is a peptidyltransferase reaction?

The transfer of the growing peptide chain from the peptidyl site to the amino acid on the aminoacyl site.

What is (approximately) the rate of peptide elongation in a ribsome?

Three to five amino acids added per second

True or false: When an mRNA stop codon is reached during translation, tRNA sends the termination base to end elongation.

False; no tRNA molecules respond to the stop codon - elongation ceases upon reaching the stop codon due to termination factors.

In translation, interaction with release factors results in ______ of the complete protein chain from the tRNA in the __ site.

Cleavage; P-site

What are chaperones?

Proteins responsible for folding a new protein into its three-dimensional shape.

What is a 'charged' tRNA molecule?

A tRNA that has been covalently attached to the correct AA on its 3' end.

What is another term meaning 'charged tRNA'?

Aminoacyl-tRNA

What enzyme charges aminoacyl-tRNA?

Aminoacyl-tRNA synthetase

What are the two major points at which the fidelity of translation is determined?

1. Synthesis of cognate amino acid/tRNA pairs by aminoacyl-tRNA synthetase in an aminoacylation reaction
2. The accuracy of aminoacyl-tRNA selection by the ribosome.

____________ are the only components of the translation machinery that really know the genetic code and are thus crucial guarantors of the ______ of protein synthesis.

Aminoacyl tRNA sythetases; fidelity

The first blank is three words

True or False: There is more than one amino acid for one codon.

False; there is more than one codon for each amino acid

How many different aminoacyl-tRNA synthetases do cells usually make?

20 - one for each type of amino acid

True or false: All aaRS are homodimers.

False; aaRS can be homodimers, small or large monomers, or tetramers (or more) of one or more different types of subunits.

What is the significance of an aaRS being a homodimer?

It can charge two tRNAs at once.

What (in general) are the differences between Class 1 and Class 2 aminoacyl-tRNA synthetases?

Class 1 is generally made up of monomers or homodimers (less complex).
Class 2 aaRS always have 2 or more subunits that are often different types (more complex).

Which of the following aaRS would be class 1? Class 2?
1. alpha
2. alpha2beta2

#1 is class 1, and #2 is class two.

Class 2 is more complex.

What are characterisics of Class 1 aminoacyl-tRNA synthetases?

-mostly monomeric
-approach tRNA along the minor groove and add AA to the 2' hydroxy of the tRNA
-class 1 aaRS have a catalytic domain structure in common (Rossmann fold)(different from class 2)

What are characteristics of Class 2 aminoacyl-tRNA synthetases?

-mostly dimeric or multimeric
-add the AA to the 3' hydroxyl site on the last tRNA base
-Class 2 aaRS have similar domain structures

Positive interactions match up the proper tRNA with the proper enzyme (synthetase).
Negative interactions block the binding of improper pairs.

How many active sites do aminoacyl-tRNA sythetases have? What are they?

aaRS have two active sites:
1. Acylation site (aka catalytic site): rejects AA that are larger than the correct one (and/or too hydrophobic/hydrophilic)
2. Editing (or "hydrolytic") site: cleaves activated species that are smaller than the correct one

What are the two basic steps in aminoacylation?

1. The AA and ATP form aminoacyl-AMP. (diphosphate product)
2. The tRNA covalently bonds to the AA, displacing AMP

In an aminoacylation reaction, what is the intermediate?

Aminoacyl-AMP (plus diphosphate)

Complete the two reactions from step one and two of an aminoacylation reaction:

Amino acid + ATP -->

Aminoacyl-AMP + tRNA -->

AA + ATP = aminoacyl-AMP + PPi

Aminoacyl-AMP + tRNA = aminoacyl-tRNA + AMP

In an acylation reaction, what type of bond is created between the carboxyl group of an AA and the 2' (class 1) or 3' (class 2) OH of the tRNA? What catalyzes this reaction?

An ester bond; catalyzed by aminoacyl-tRNA sythetase

What happens in step 1 of an acylation reaction? In step 2?

Step 1:
-the enzyme (sythetase) binds ATP and the AA, catalyzing the formation of an aminoacyl-adenylate intermediate (Aminoacyl-AMP).
-the intermediate is formed by a covalent linkage between the 5' phosphate group of ATP and the carboxyl end of the AA.
-when ATP is hydrolyzed, the aminoacyl tRNA sythetase uses the energy to activate the amino acid, forming the intermediate.
-the sythetase remains associated with the intermediate.

Step 2:
-the 2' or 3' OH of the terminal adenosine of tRNA attacks the amino acid carbonyl carbon atom, and the amino acid is transferred to the appropriate tRNA.
-The amino acid is covalently bonded to either the 2' OH or 3'OH (depending on sythetase) of the INVARIANT 3' adenosine terminal of the tRNA molecule.
-The energy in the aminoacyl-AMP is used to transfer the amino acid to the tRNA, forming aminoacyl-tRNA.

After step 1 of an acylation reaction, why is the amino acid call an 'activated' amino acid?

Because when ATP is hydrolyzed, the high energy bonds between the phosphate groups are broken, and the energy is trapped in the aminoacyl-AMP intermediate.

a. the small subunit of the prokaryotic ribosome
b. the small subunit of the eukaryotic ribosome
c. the eukaryotic ribosome (whole)
d. the large subunit of the prokaryotic ribosome
e. the large subunit of the eukaryotic ribosome
f. the prokaryotic ribosome (whole)

If in eukaryotic ribosomes, the large subunit is 60S and the small subunit is 40S, what is the entire ribosome referred to as?

80S

If in prokaryotic ribosomes, the large subunit is 50S and the small subunit is 30S, what is the entire ribsome referred to as?

70S

What is the dominant activity of almost all cells?

Ribosomal activity (90% of cell energy in prokaryotes)

What are some characteristics of the large subunit of the ribosome?

-composed of two RNA strands
-contains the active site (where the new peptide bonds are created when proteins are synthesized)
-dozens of proteins bind on the surface of the ribosome
-the interaction of the RNA and proteins give the ribosome its structural integrity.

What are some characteristics of the small subunit in a ribosome?

-in charge of information flow during protein synthesis
-initially finds mRNA strand
-after combining with large subunit, ensures each codon in message is paired with the anticodon in the proper tRNA

During translation, the mRNA enters through a small hole in the ______ ribosomal subunit.

Through a small hole formed by a loop of rRNA, which can open and admit the messenger.

How many active sites exist in a ribosome? What are they?

3 active sites:
Two sites for binding charged tRNA:
1. A (aminoacyl/acceptor) site: exposes the codon for the next AA to be added to the growing chain, then binds to the incoming aminoacyl-tRNA.
2. P (peptidyl/donor) site: occupied by the peptidyl-tRNA, a tRNA carrying the growing polypeptide chain

Site for uncharged tRNA:
3. the E (exit) site: where tRNA exits after being separated from its AA

What order do tRNA (except the initial Met. tRNA) follow in translation (active sites)?

A-P-E; A and P hold charged tRNAs, E releases uncharged tRNA

What is a polysome?

An mRNA with more than one ribosomal subunit

What direction, 3' to 5' or 5' to 3', does translation move in?

5' to 3'

In translation, proteins are sythesized from the _________ end to the __________ terminus.

Amino (N); Carboxy (C) - relative to the protein

What is the translational start codon?

AUG

You should know this

What are the two types of tRNA (methionine) molecules in the cell? What type of tRNA sythetases charge these tRNAs?